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- PDB-7rma: Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKR... -

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Basic information

Entry
Database: PDB / ID: 7rma
TitleStructure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a high affinity UbV (Ubiquitin Variant)
Components
  • Ankyrin repeat domain-containing protein 13D
  • Ubiquitin Variant
KeywordsPROTEIN BINDING / Ubiquitin-interacting motif / UIM / Ubiquitin Variant / protein engineering / protein recognition / strand-exchange dimer
Function / homology
Function and homology information


negative regulation of receptor internalization / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / ubiquitin-modified protein reader activity / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...negative regulation of receptor internalization / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / ubiquitin-modified protein reader activity / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity
Similarity search - Function
Ankyrin repeat domain-containing protein 13 / GPCR-chaperone / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ankyrin repeat domain-containing protein 13 / GPCR-chaperone / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ankyrin repeat domain-containing protein 13D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSinger, A.U. / Manczyk, N. / Veggiani, G. / Sicheri, F. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Ontario Research Fund72056614 Canada
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs.
Authors: Veggiani, G. / Yates, B.P. / Martyn, G.D. / Manczyk, N. / Singer, A.U. / Kurinov, I. / Sicheri, F. / Sidhu, S.S.
History
DepositionJul 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin Variant
C: Ankyrin repeat domain-containing protein 13D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3944
Polymers12,2752
Non-polymers1192
Water30617
1
A: Ubiquitin Variant
C: Ankyrin repeat domain-containing protein 13D
hetero molecules

A: Ubiquitin Variant
C: Ankyrin repeat domain-containing protein 13D
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Only half of the 2:2 complex is in the unit cell -- the other half is generated by the second of the translation/rotation matrices listed below. Gel filtration was used to ...Evidence: gel filtration, Only half of the 2:2 complex is in the unit cell -- the other half is generated by the second of the translation/rotation matrices listed below. Gel filtration was used to purify this Ubv, which in the absence of peptide, ran as a dimer
  • 24.8 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)24,7888
Polymers24,5504
Non-polymers2384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7810 Å2
ΔGint-79 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.770, 45.770, 84.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

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Components

#1: Protein Ubiquitin Variant


Mass: 9849.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: phage display from wild-type ubiquitin / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pHH239
Details (production host): TEV cleavage released the N-terminus which contained a 6-His affinity tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#2: Protein/peptide Ankyrin repeat domain-containing protein 13D


Mass: 2425.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6ZTN6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Li2SO4, 0.1M sodium acetate pH 4.5 and 50% PEG 400. Crystals were cryoprotected in this buffer plus 20% ethylene glycol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→32.36 Å / Num. obs: 6724 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.077 / Net I/σ(I): 14
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 448 / CC1/2: 0.953 / Rsym value: 0.595 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UbV from PDB 6CRN

6crn


Resolution: 2→32.36 Å / SU ML: 0.2217 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.0478 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2464 648 10 %
Rwork0.2077 5834 -
obs0.2119 6482 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.37 Å2
Refinement stepCycle: LAST / Resolution: 2→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 0 6 17 769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064780
X-RAY DIFFRACTIONf_angle_d0.72551058
X-RAY DIFFRACTIONf_chiral_restr0.0522122
X-RAY DIFFRACTIONf_plane_restr0.0055139
X-RAY DIFFRACTIONf_dihedral_angle_d19.3274483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.29271250.27311128X-RAY DIFFRACTION99.44
2.15-2.370.34281250.24921132X-RAY DIFFRACTION99.29
2.37-2.710.26641290.24251150X-RAY DIFFRACTION99.77
2.71-3.420.21391300.21911169X-RAY DIFFRACTION99.39
3.42-32.360.23261390.1781255X-RAY DIFFRACTION99.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.144006893932.34627796503-2.147160324514.19602678435-3.762156831573.348429310110.2071717473530.697629071220.4830408783120.0845896887534-0.02187902860670.464462805694-0.6300591908640.331587812531-0.240608209920.533659921469-0.0509552576559-0.04389707425720.3933303507540.07898093693820.2633895550714.57816100264.6427887045122.3466721367
22.275590697330.00854490396605-1.189834317952.14753819566-0.9917459400981.07787599381-0.1123188228310.0189203160097-0.4305298883160.028280736278-0.3135918233420.427300059191-0.597364311023-1.470182829170.01750347348580.3266620969940.01129098494810.08460381512691.10015154937-0.09197124265620.414854817519-10.2623043455-12.917120559619.8927408861
35.263498391761.74828966738-2.559973137996.14650331153.221742220346.11835973489-0.552095527245-0.2297373749320.536067817340.823195417874-0.2731668356020.889114758618-0.2125076002680.2420320971140.07853273888310.4567585795530.3442941479990.1190019328341.06928190084-0.1397628976980.339932577574-9.81154552031-5.0843984104618.568698891
44.737098030510.6957833153120.9730736976077.027146443483.821589785939.04741645554-0.148828416053-0.114751582198-0.0114518301487-0.602416209807-0.300469143330.450159837038-0.0547847915816-1.252039964280.3707593356920.317044615096-0.03971350966080.02812234392770.513900040504-0.08640500043270.241567441857-6.51916605891-11.250918974310.9441531265
56.18300825452.527324280340.8287570633132.44775871066-2.143125541756.840099334330.0640247801951-0.271427787010.484571787153-0.0361032173992-0.8288207158930.0929294062763-0.900697076590.01094317591250.4765217286670.3865578397760.0431480124407-0.04747129871670.25407441395-0.06559025751650.2358119228932.14539570064-3.9671763496213.752086491
64.928795856951.282865770065.001832152093.94238649865.379588899.65396972904-0.00167898302371-0.162455064837-0.02258300985120.5683441077170.0746226104131-0.03831874210820.186501173478-0.0338245692705-0.05947290331760.342963432204-0.03299431281980.1183569729010.250705852431-0.02790485082090.2407810841396.96013307002-12.244413444710.1207560687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 34 )
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 74 )
6X-RAY DIFFRACTION6chain 'C' and (resid 4 through 22 )

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